On Monday, November 28, 2011, Joseph Hargitai
joseph.hargi...@einstein.yu.edu wrote:
Ed,
we had the classic goof on our cluster with this. 4 nodes could not see
the /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs
hit those nodes (which explains the randomness) we got
Aurelien,
The particular behavior that you need isn't currently supported because the
value of from_work_dir isn't treated as a template. To work around this
limitation, you can do the move/copy operations in your tool wrapper; see
the wrappers for Bowtie and Sicer for examples on how to
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the delete 'X' icon near the
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in
universe_wsgi.ini?
Please see this wiki for details:
http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen
Galaxy team
On
Folks,
I was writing a samtools/mpileup wrapper for our local use. When I delved into
how the existing samtools/sam_pileup.py adaptor worked, if found that it has a
local copy of the routine to look up the samtools .fai file in
sam_fa_indices.loc for installed genomes. I then noticed that this
Hi,
I'm testing the GATK pipeline and I ran into a problem with Variant
Recalibrator tool. It seems I don't have correctly configure R and
GATK on my instance, as this tool is failing with this error:
mv:
/Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat.pdf:
No such
I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question .
When I try to Get Data from UCSC or any other external site, I get a 407
error from our proxy as I need to authenticate.
Is the request going out as the 'galaxy' user or 'apache' or the user that's
logged in?
I
Curtis,
[curtish@cheaha galaxy]$ find . -name *.py | xargs grep sam_fa_indices.loc
./tools/samtools/sam_pileup.py:seqFile = '%s/sam_fa_indices.loc' %
GALAXY_DATA_INDEX_DIR
...
./tools/ngs_rna/cufflinks_wrapper_without_gtf.py:
cached_seqs_pointer_file = os.path.join(
Hello,
Perhaps you have found this in the source already, but if not, a version
of the Tophat tool for SOLiD is available. It is on the test server
only, should be used with caution, and is completely unsupported.
In the Galaxy source at bitbucket, please see:
tophat_color_wrapper.xml at
Hello,
In case you have not found the answers in the wiki yet, a link to the
administration details for data libraries are:
General/All:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries
Loading Data:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Hopefully this
Hello Bernhard,
I came across your question and see that you may never have had a reply.
If you have this already worked out, then great! But if not, perhaps the
API wikis will be of interest:
http://galaxyproject.org/wiki/Learn/API
The documentation is still in progress, but the main
Hello Candace,
Hopefully you have already discovered this, but genomes can be loaded
(usually using FTP) into a history and used as a custom genome with many
tools. The genomes are loaded in fasta format and indexes are generated
by the tools themselves. Most tools that use a reference genome
On Nov 29, 2011, at 3:13 AM, Peter Cock wrote:
On Monday, November 28, 2011, Joseph Hargitai
joseph.hargi...@einstein.yu.edu wrote:
Ed,
we had the classic goof on our cluster with this. 4 nodes could not see the
/home/galaxy folder due to a missing entry in /etc/fstab. When the jobs
Hello David,
Renaming with incremental numerical sequence (or with sequence), as you
did originally with the tool NGS: QC and manipulation - FASTX-Toolkit
for FASTQ data - Rename sequences, is the current option.
If your or someone else following Q/A on the list develops a tool that
offers
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